Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression.

Tuechler N, Burtscher LM, Garrido-Rodriguez M, Khan MM, Turei D, Tischer C, Kaspar S, Schwarz JJ, Stein F, Rettel M, Kramann R, Savitski MM, Saez-Rodriguez J, Pepperkok R

bioRxiv, 2025

doi:10.1101/2024.10.15.618507.

Jumbo phage killer immune system targets early infection of nucleus-forming phages.

Yuping L, Guan L, Becher I, Makarova KS, Cao X, Hareendranath S, Guan J, Stein F, Yang S, Boergel A, Lapouge K, Remans K, Agard D, Savitski M, Typas A, Koonin EV, Feng Y, Bondy-Denomy J

Cell, 2025

doi:10.1016/j.cell.2025.02.016.

Uncovering protein glycosylation dynamics and heterogeneity using deep quantitative glycoprofiling (DQGlyco).

Potel CM, Burtscher ML, Garrido-Rodriguez M, Brauer-Nikonow A, Becher I, Le Sueur C, Typas A, Zimmermann M, Savitski MM

Nature structural & molecular biology, 2025

doi:10.1038/s41594-025-01485-w.

Longitudinal omics data and preclinical treatment suggest the proteasome inhibitor carfilzomib as therapy for ibrutinib-resistant CLL.

Arseni L, Sigismondo G, Yazdanparast H, Hermansen JU, Mack N, Ohl S, Kalter V, Iskar M, Kalxdorf M, Friedel D, Rettel M, Paul Y, Ringshausen I, Eldering E, Dubois J, Kater AP, Zapatka M, Roessner PM, Tausch E, Stilgenbauer S, Dietrich S, Savitski MM, Skånland SS, Krijgsveld J, Lichter P, Seiffert M

Nature communications, 2025

doi:10.1038/s41467-025-56318-7.

R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning.

Brenes-Álvarez M, Ropp HR, Papagiannidis D, Potel CM, Stein F, Scholz I, Steglich C, Savitski MM, Vioque A, Muro-Pastor AM, Hess WR

Nucleic acids research, 2025

doi:10.1093/nar/gkae1247.

Dextromethorphan inhibits collagen and collagen-like cargo secretion to ameliorate lung fibrosis.

Khan MM, Galea G, Jung J, Zukowska J, Lauer D, Tuechler N, Halavatyi A, Tischer C, Haberkant P, Stein F, Jung F, Landry JJM, Khan AM, Oorschot V, Becher I, Neumann B, Muley T, Winter H, Duerr J, Mall MA, Grassi A, de la Cueva E, Benes V, Gote-Schniering J, Savitski M, Pepperkok R

Science translational medicine, 2024

doi:10.1126/scitranslmed.adj3087.

Salmonella infection impacts host proteome thermal stability.

Birk MS, Walch P, Baykara T, Sefried S, Amelang J, Buerova E, Breuer I, Vervoots J, Typas A, Savitski MM, Mateus A, Selkrig J

European journal of cell biology, 2024

doi:10.1016/j.ejcb.2024.151448.

Emergence of community behaviors in the gut microbiota upon drug treatment.

Garcia-Santamarina S, Kuhn M, Devendran S, Maier L, Driessen M, Mateus A, Mastrorilli E, Brochado AR, Savitski MM, Patil KR, Zimmermann M, Bork P, Typas A

Cell, 2024

doi:10.1016/j.cell.2024.08.037.

Pervasive sublethal effects of agrochemicals on insects at environmentally relevant concentrations.

Gandara L, Jacoby R, Laurent F, Spatuzzi M, Vlachopoulos N, Borst NO, Ekmen G, Potel CM, Garrido-Rodriguez M, Böhmert AL, Misunou N, Bartmanski BJ, Li XC, Kutra D, Hériché JK, Tischer C, Zimmermann-Kogadeeva M, Ingham VA, Savitski MM, Masson JB, Zimmermann M, Crocker J

Science (New York, N.Y.), 2024

doi:10.1126/science.ado0251.

LD-transpeptidation is crucial for fitness and polar growth in Agrobacterium tumefaciens.

Aliashkevich A, Guest T, Alvarez L, Gilmore MC, Rea D, Amstutz J, Mateus A, Schiffthaler B, Ruiz I, Typas A, Savitski MM, Brown PJB, Cava F

PLoS genetics, 2024

doi:10.1371/journal.pgen.1011449.

GPMelt: A hierarchical Gaussian process framework to explore the dark meltome of thermal proteome profiling experiments.

Le Sueur C, Rattray M, Savitski M

PLoS computational biology, 2024

doi:10.1371/journal.pcbi.1011632.

Essentiality of LD-Transpeptidation in Agrobacterium tumefaciens.

Aliashkevich A, Guest T, Alvarez L, Gilmore MC, Amstutz J, Mateus A, Schiffthaler B, Ruiz I, Typas A, Savitski MM, Brown PJB, Cava F

bioRxiv, 2024

doi:10.1101/2024.06.21.600065.

Uncovering nitroxoline activity spectrum, mode of action and resistance across Gram-negative bacteria.

Cacace E, Tietgen M, Steinhauer M, Mateus A, Schultze TG, Eckermann M, Galardini M, Varik V, Koumoutsi A, Parzeller JJ, Corona F, Orakov A, Knopp M, Brauer-Nikonow A, Bork P, Romao CV, Zimmermann M, Cloetens P, Savitski MM, Typas A, Göttig S

bioRxiv, 2024

doi:10.1101/2024.06.04.597298.

Systematic analysis of protein stability associated with species-specific developmental tempo.

Matsuda M, Hammarén HM, Lázaro J, Savitski MM, Ebisuya M

bioRxiv, 2024

doi:10.1101/2024.06.07.597977.

Macromolecular crowding in human tenocyte and skin fibroblast cultures: a comparative analysis.

Djalali-Cuevas A, Rettel M, Stein F, Savitski M, Kearns S, Kelly J, Biggs M, Skoufos I, Tzora A, Prassinos N, Diakakis N, Zeugolis DI

Materials Today Bio, 2024

doi:10.1016/j.mtbio.2024.100977.

Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response.

Ruperti F, Becher I, Stokkermans A, Wang L, Marschlich N, Potel C, Maus E, Stein F, Drotleff B, Schippers KJ, Nickel M, Prevedel R, Musser JM, Savitski MM, Arendt D

Current biology : CB, 2023

doi:10.1016/j.cub.2023.12.021.

Systematic analysis of drug combinations against Gram-positive bacteria.

Cacace E, Kim V, Varik V, Knopp M, Tietgen M, Brauer-Nikonow A, Inecik K, Mateus A, Milanese A, Mårli MT, Mitosch K, Selkrig J, Brochado AR, Kuipers OP, Kjos M, Zeller G, Savitski MM, Göttig S, Huber W, Typas A

Nature microbiology, 2023

doi:10.1038/s41564-023-01486-9.

STPP-UP: an alternative method for drug target identification using protein thermal stability.

Zijlmans DW, Hernández-Quiles M, Jansen PWTC, Becher I, Stein F, Savitski MM, Vermeulen M

The Journal of biological chemistry, 2023

doi:10.1016/j.jbc.2023.105279.

Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome.

Potel CM, Burtscher ML, Garrido-Rodriguez M, Brauer-Nikonow A, Becher I, Typas A, Zimmermann M, Savitski MM

bioRxiv, 2023

doi:10.1101/2023.09.13.557529.

Mitochondrial dysfunction rapidly modulates the abundance and thermal stability of cellular proteins.

Groh C, Haberkant P, Stein F, Filbeck S, Pfeffer S, Savitski MM, Boos F, Herrmann JM

Life science alliance, 2023

doi:10.26508/lsa.202201805.

D-amino acids signal a stress-dependent run-away response in Vibrio cholerae.

Irazoki O, Ter Beek J, Alvarez L, Mateus A, Colin R, Typas A, Savitski MM, Sourjik V, Berntsson RP, Cava F

Nature microbiology, 2023

doi:10.1038/s41564-023-01419-6.

Dual truncation of tau by caspase-2 accelerates its CHIP-mediated degradation.

Reinhardt L, Musacchio F, Bichmann M, Behrendt A, Ercan-Herbst E, Stein J, Becher I, Haberkant P, Mader J, Schöndorf DC, Schmitt M, Korffmann J, Reinhardt P, Pohl C, Savitski M, Klein C, Gasparini L, Fuhrmann M, Ehrnhoefer DE

Neurobiology of disease, 2023

doi:10.1016/j.nbd.2023.106126.

Defining basic rules for hardening influenza A virus liquid condensates.

Etibor TA, Vale-Costa S, Sridharan S, Brás D, Becher I, Mello VH, Ferreira F, Alenquer M, Savitski MM, Amorim MJ

eLife, 2023

doi:10.7554/elife.85182.

Molecular mechanisms of stress-induced reactivation in mumps virus condensates.

Zhang X, Sridharan S, Zagoriy I, Eugster Oegema C, Ching C, Pflaesterer T, Fung HKH, Becher I, Poser I, Müller CW, Hyman AA, Savitski MM, Mahamid J

Cell, 2023

doi:10.1016/j.cell.2023.03.015.

Deep thermal profiling for detection of functional proteoform groups.

Kurzawa N, Leo IR, Stahl M, Kunold E, Becher I, Audrey A, Mermelekas G, Huber W, Mateus A, Savitski MM, Jafari R

Nature chemical biology, 2023

doi:10.1038/s41589-023-01284-8.

Control of protein stability by post-translational modifications.

Lee JM, Hammarén HM, Savitski MM, Baek SH

Nature communications, 2023

doi:10.1038/s41467-023-35795-8.

PLDMS: Phosphopeptide library dephosphorylation followed by mass spectrometry analysis to determine the specificity of phosphatases for dephosphorylation site sequences.

Kokot T, Hoermann B, Helm D, Chojnacki JE, Savitski MM, Köhn M

Methods in molecular biology (Clifton, N.J.), 2022

doi:10.1007/978-1-0716-2317-6_2.

Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation.

Hammarén HM, Geissen EM, Potel CM, Beck M, Savitski MM

Nature communications, 2022

doi:10.1038/s41467-022-35054-2.

Thermal proteome profiling: insights into protein modifications, associations, and functions.

Le Sueur C, Hammarén HM, Sridharan S, Savitski MM

Current opinion in chemical biology, 2022

doi:10.1016/j.cbpa.2022.102225.

Transient glycolytic complexation of arsenate enhances resistance in the enteropathogen Vibrio cholerae.

Bueno E, Pinedo V, Shinde DD, Mateus A, Typas A, Savitski MM, Thomas VC, Cava F

mBio, 2022

doi:10.1128/mbio.01654-22.

Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements.

Ibarra IL, Ratnu VS, Gordillo L, Hwang IY, Mariani L, Weinand K, Hammarén HM, Heck J, Bulyk ML, Savitski MM, Zaugg JB, Noh KM

Molecular systems biology, 2022

doi:10.15252/msb.202110473.

Systematic discovery of biomolecular condensate-specific protein phosphorylation.

Sridharan S, Hernandez-Armendariz A, Kurzawa N, Potel CM, Memon D, Beltrao P, Bantscheff M, Huber W, Cuylen-Haering S, Savitski MM

Nature chemical biology, 2022

doi:10.1038/s41589-022-01062-y.

Bacterial retrons encode phage-defending tripartite toxin-antitoxin systems.

Bobonis J, Mitosch K, Mateus A, Karcher N, Kritikos G, Selkrig J, Zietek M, Monzon V, Pfalz B, Garcia-Santamarina S, Galardini M, Sueki A, Kobayashi C, Stein F, Bateman A, Zeller G, Savitski MM, Elfenbein JR, Andrews-Polymenis HL, Typas A

Nature, 2022

doi:10.1038/s41586-022-05091-4.

Dendritic autophagy degrades postsynaptic proteins and is required for long-term synaptic depression in mice.

Kallergi E, Daskalaki AD, Kolaxi A, Camus C, Ioannou E, Mercaldo V, Haberkant P, Stein F, Sidiropoulou K, Dalezios Y, Savitski MM, Bagni C, Choquet D, Hosy E, Nikoletopoulou V

Nature communications, 2022

doi:10.1038/s41467-022-28301-z.

High-throughput functional characterization of protein phosphorylation sites in yeast.

Viéitez C, Busby BP, Ochoa D, Mateus A, Memon D, Galardini M, Yildiz U, Trovato M, Jawed A, Geiger AG, Oborská-Oplová M, Potel CM, Vonesch SC, Szu Tu C, Shahraz M, Stein F, Steinmetz LM, Panse VG, Noh KM, Savitski MM, Typas A, Beltrao P

Nature biotechnology, 2021

doi:10.1038/s41587-021-01051-x.

Drug target identification in tissues by thermal proteome profiling.

Mateus A, Kurzawa N, Perrin J, Bergamini G, Savitski MM

Annual review of pharmacology and toxicology, 2021

doi:10.1146/annurev-pharmtox-052120-013205.

Bioaccumulation of therapeutic drugs by human gut bacteria.

Klünemann M, Andrejev S, Blasche S, Mateus A, Phapale P, Devendran S, Vappiani J, Simon B, Scott TA, Kafkia E, Konstantinidis D, Zirngibl K, Mastrorilli E, Banzhaf M, Mackmull MT, Hövelmann F, Nesme L, Brochado AR, Maier L, Bock T, Periwal V, Kumar M, Kim Y, Tramontano M, Schultz C, Beck M, Hennig J, Zimmermann M, Sévin DC, Cabreiro F, Savitski MM, Bork P, Typas A, Patil KR

Nature, 2021

doi:10.1038/s41586-021-03891-8.

Transcriptional and post-transcriptional polar effects in bacterial gene deletion libraries.

Mateus A, Shah M, Hevler J, Kurzawa N, Bobonis J, Typas A, Savitski MM

mSystems, 2021

doi:10.1128/mSystems.00813-21.

The rise of proteome-wide biophysics.

Mateus A, Savitski MM, Piazza I

Molecular systems biology, 2021

doi:10.15252/msb.202110442.

Structure and dynamics of the quaternary hunchback mRNA translation repression complex.

Macošek J, Simon B, Linse JB, Jagtap PKA, Winter SL, Foot J, Lapouge K, Perez K, Rettel M, Ivanović MT, Masiewicz P, Murciano B, Savitski MM, Loedige I, Hub JS, Gabel F, Hennig J

Nucleic acids research, 2021

doi:10.1093/nar/gkab635.

Structure of the mycobacterial ESX-5 type VII secretion system pore complex.

Beckham KSH, Ritter C, Chojnowski G, Ziemianowicz DS, Mullapudi E, Rettel M, Savitski MM, Mortensen SA, Kosinski J, Wilmanns M

Science advances, 2021

doi:10.1126/sciadv.abg9923.

Impact of phosphorylation on thermal stability of proteins.

Potel CM, Kurzawa N, Becher I, Typas A, Mateus A, Savitski MM

Nature methods, 2021

doi:10.1038/s41592-021-01177-5.

Global mapping of Salmonella enterica-host protein-protein interactions during infection.

Walch P, Selkrig J, Knodler LA, Rettel M, Stein F, Fernandez K, Viéitez C, Potel CM, Scholzen K, Geyer M, Rottner K, Steele-Mortimer O, Savitski MM, Holden DW, Typas A

Cell Host and Microbe, 2021

doi:10.1016/j.chom.2021.06.004.

SARS-CoV-2 infection remodels the host protein thermal stability landscape.

Selkrig J, Stanifer M, Mateus A, Mitosch K, Barrio-Hernandez I, Rettel M, Kim H, Voogdt CGP, Walch P, Kee C, Kurzawa N, Stein F, Potel C, Jarzab A, Kuster B, Bartenschlager R, Boulant S, Beltrao P, Typas A, Savitski MM

Molecular systems biology, 2021

doi:10.15252/msb.202010188.

Cell surface thermal proteome profiling tracks perturbations and drug targets on the plasma membrane.

Kalxdorf M, Günthner I, Becher I, Kurzawa N, Knecht S, Savitski MM, Eberl HC, Bantscheff M

Nature methods, 2021

doi:10.1038/s41592-020-01022-1.

A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles.

Kurzawa N, Becher I, Sridharan S, Franken H, Mateus A, Anders S, Bantscheff M, Huber W, Savitski MM

Nature communications, 2020

doi:10.1038/s41467-020-19529-8.

The functional proteome landscape of Escherichia coli.

Mateus A, Hevler J, Bobonis J, Kurzawa N, Shah M, Mitosch K, Goemans CV, Helm D, Stein F, Typas A, Savitski MM

Nature, 2020

doi:10.1038/s41586-020-3002-5.

Aggregation and disaggregation features of the human proteome.

Määttä TA, Rettel M, Sridharan S, Helm D, Kurzawa N, Stein F, Savitski MM

Molecular systems biology, 2020

doi:10.15252/msb.20209500.

Rtpca: an R package for differential thermal proximity coaggregation analysis.

Kurzawa N, Mateus A, Savitski MM

Bioinformatics (Oxford, England), 2020

doi:10.1093/bioinformatics/btaa682.

Pseudo-RNA-binding domains mediate RNA structure specificity in Upstream of N-Ras.

Hollmann NM, Jagtap PKA, Masiewicz P, Guitart T, Simon B, Provaznik J, Stein F, Haberkant P, Sweetapple LJ, Villacorta L, Moojiman D, Benes V, Savitski MM, Gebauer F, Hennig J

2020

doi:10.1016/j.celrep.2020.107930.

Dissecting the sequence determinants for dephosphorylation by the catalytic subunits of phosphatases PP1 and PP2A.

Hoermann B, Kokot T, Helm D, Heinzlmeir S, Chojnacki JE, Schubert T, Ludwig C, Berteotti A, Kurzawa N, Kuster B, Savitski MM, Köhn M

Nature communications, 2020

doi:10.1038/s41467-020-17334-x.

Spatiotemporal proteomics uncovers cathepsin-dependent macrophage cell death during Salmonella infection.

Selkrig J, Li N, Hausmann A, Mangan MSJ, Zietek M, Mateus A, Bobonis J, Sueki A, Imamura H, El Debs B, Sigismondo G, Florea BI, Overkleeft HS, Kopitar-Jerala N, Turk B, Beltrao P, Savitski MM, Latz E, Hardt WD, Krijgsveld J, Typas A

Nature microbiology, 2020

doi:10.1038/s41564-020-0736-7.

Phage proteins block and trigger retron toxin/antitoxin systems.

Bobonis J, Mitosch K, Mateus A, Kritikos G, Elfenbein JR, Savitski MM, Andrews-Polymenis H, Typas A

bioRxiv, 2020

doi:10.1101/2020.06.22.160242.

A dual-mechanism antibiotic kills gram-negative bacteria and avoids drug resistance.

Martin JK, Sheehan JP, Bratton BP, Moore GM, Mateus A, Li SH, Kim H, Rabinowitz JD, Typas A, Savitski MM, Wilson MZ, Gitai Z

Cell, 2020

doi:10.1016/j.cell.2020.05.005.

Meltome atlas-thermal proteome stability across the tree of life.

Jarzab A, Kurzawa N, Hopf T, Moerch M, Zecha J, Leijten N, Bian Y, Musiol E, Maschberger M, Stoehr G, Becher I, Daly C, Samaras P, Mergner J, Spanier B, Werner T, Angelov A, Wilhelm M, Bantscheff M, Lemeer S, Klingenspor M, Hahne H, Liebl W, Kuster B, Savitski MM

Nature methods, 2020

doi:10.1038/s41592-020-0801-4.

Thermal proteome profiling for interrogating protein interactions.

Mateus A, Kurzawa N, Becher I, Sridharan S, Helm D, Stein F, Typas A, Savitski MM

Molecular systems biology, 2020

doi:10.15252/msb.20199232.

Systematic localization of Escherichia coli membrane proteins.

Sueki A, Stein F, Savitski MM, Selkrig J, Typas A

mSystems, 2020

doi:10.1128/mSystems.00808-19.

A genetic analysis reveals novel histone residues required for transcriptional reprogramming upon stress.

Viéitez C, Martínez-Cebrián G, Solé C, Böttcher R, Potel CM, Savitski MM, Onnebo S, Fabregat M, Shilatifard A, Posas F, de Nadal E

Nucleic acids research, 2020

doi:10.1093/nar/gkaa081.

Outer membrane lipoprotein NlpI scaffolds peptidoglycan hydrolases within multi-enzyme complexes in Escherichia coli.

Banzhaf M, Yau HC, Verheul J, Lodge A, Kritikos G, Mateus A, Cordier B, Hov AK, Stein F, Wartel M, Pazos M, Solovyova AS, Breukink E, van Teeffelen S, Savitski MM, den Blaauwen T, Typas A, Vollmer W

The EMBO journal, 2020

doi:10.15252/embj.2019102246.

A misprocessed form of Apolipoprotein A-I is specifically associated with recurrent focal segmental glomerulosclerosis.

Jacobs-Cachá C, Puig-Gay N, Helm D, Rettel M, Sellarès J, Meseguer A, Savitski MM, Moreso FJ, Soler MJ, Seron D, Lopez-Hellin J

Scientific reports, 2020

doi:10.1038/s41598-020-58197-y.

Identifying drug targets in tissues and whole blood with thermal-shift profiling.

Perrin J, Werner T, Kurzawa N, Rutkowska A, Childs DD, Kalxdorf M, Poeckel D, Stonehouse E, Strohmer K, Heller B, Thomson DW, Krause J, Becher I, Eberl HC, Vappiani J, Rau CE, Sevin DC, Huber W, Franken H, Savitski MM, Faelth-Savitski M, Bergamini G, Bantscheff M

Nature biotechnology, 2020

doi:10.1038/s41587-019-0388-4.

Towards a systematic map of the functional role of protein phosphorylation.

Viéitez​ C​, Busby​ BP, Ochoa​ D​, Mateus​ A​, Galardini​ M​, Jawed​ A​, Memon​ D​, Potel​ CM​, Vonesch SC​, Tu​ CS, Shahraz​ M​, Stein​ F​, Steinmetz​ LM, Savitski​ MM, Typas A, Beltrao​ P

bioRxiv, 2019

doi:10.1101/872770.

The functional landscape of the human phosphoproteome.

Ochoa D, Jarnuczak AF, Viéitez C, Gehre M, Soucheray M, Mateus A, Kleefeldt AA, Hill A, Garcia-Alonso L, Stein F, Krogan NJ, Savitski MM, Swaney DL, Vizcaíno JA, Noh KM, Beltrao P

Nature biotechnology, 2019

doi:10.1038/s41587-019-0344-3.

A new antibiotic selectively kills Gram-negative pathogens.

Imai Y, Meyer KJ, Iinishi A, Favre-Godal Q, Green R, Manuse S, Caboni M, Mori M, Niles S, Ghiglieri M, Honrao C, Ma X, Guo J, Makriyannis A, Linares-Otoya L, Wuisan ZG, Böhringer N, Wu R, Kaur H, Typas A, Mateus A, Espinoza JL, Savitski MM, Nelson KE, O'Rourke A, Noinaj N, Hiller S, D'Onofrio A, Schäberle TF, Lewis K

Nature, 2019

doi:10.1038/s41586-019-1791-1.

Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins.

Childs D, Bach K, Franken H, Anders S, Kurzawa N, Bantscheff M, Savitski M, Huber W

Molecular & cellular proteomics : MCP, 2019

doi:10.1074/mcp.TIR119.001481.

Target discovery using thermal proteome profiling.

Sridharan S, Günthner I, Becher I, Savitski M, Bantscheff M

2019

doi:10.1002/9781118970195.ch11.

Mitochondrial protein-induced stress triggers a global adaptive transcriptional programme.

Boos F, Krämer L, Groh C, Jung F, Haberkant P, Stein F, Wollweber F, Gackstatter A, Zöller E, van der Laan M, Savitski MM, Benes V, Herrmann JM

Nature cell biology, 2019

doi:10.1038/s41556-019-0294-5.

Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP.

Sridharan S, Kurzawa N, Werner T, Günthner I, Helm D, Huber W, Bantscheff M, Savitski MM

Nature communications, 2019

doi:10.1038/s41467-019-09107-y.

Effect of Sec61 interaction with Mpd1 on endoplasmic reticulum-associated degradation.

Pereira F, Rettel M, Stein F, Savitski MM, Collinson I, Römisch K

PloS one, 2019

doi:10.1371/journal.pone.0211180.

Thermal proteome profiling in bacteria: probing protein state in vivo.

Mateus A, Bobonis J, Kurzawa N, Stein F, Helm D, Hevler J, Typas A, Savitski MM

Molecular systems biology, 2018

doi:10.15252/msb.20188242.

Species-specific activity of antibacterial drug combinations.

Brochado AR, Telzerow A, Bobonis J, Banzhaf M, Mateus A, Selkrig J, Huth E, Bassler S, Zamarreño Beas J, Zietek M, Ng N, Foerster S, Ezraty B, Py B, Barras F, Bork P, Savitski MM, Göttig S, Typas A

Nature, 2018

doi:10.1038/s41586-018-0278-9.

TRRAP is essential for regulating the accumulation of mutant and wild-type p53 in lymphoma.

Jethwa A, Słabicki M, Hüllein J, Jentzsch M, Dalal V, Rabe S, Wagner L, Walther T, Klapper W, Bohnenberger H, Rettel M, Lu J, Smits AH, Stein F, Savitski MM, Huber W, Aylon Y, Oren M, Zenz T

Blood, 2018

doi:10.1182/blood-2017-09-806679.

Pervasive protein thermal stability variation during the cell cycle.

Becher I, Andrés-Pons A, Romanov N, Stein F, Schramm M, Baudin F, Helm D, Kurzawa N, Mateus A, Mackmull MT, Typas A, Müller CW, Bork P, Beck M, Savitski MM

Cell, 2018

doi:10.1016/j.cell.2018.03.053.

Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis.

Savitski MM, Zinn N, Faelth-Savitski M, Poeckel D, Gade S, Becher I, Muelbaier M, Wagner AJ, Strohmer K, Werner T, Melchert S, Petretich M, Rutkowska A, Vappiani J, Franken H, Steidel M, Sweetman GM, Gilan O, Lam EYN, Dawson MA, Prinjha RK, Grandi P, Bergamini G, Bantscheff M

Cell, 2018

doi:10.1016/j.cell.2018.02.030.

Systematic analysis of protein turnover in primary cells.

Mathieson T, Franken H, Kosinski J, Kurzawa N, Zinn N, Sweetman G, Poeckel D, Ratnu VS, Schramm M, Becher I, Steidel M, Noh KM, Bergamini G, Beck M, Bantscheff M, Savitski MM

Nature communications, 2018

doi:10.1038/s41467-018-03106-1.

Leaderless secreted peptide signaling molecule alters global gene expression and increases virulence of a human bacterial pathogen.

Do H, Makthal N, VanderWal AR, Rettel M, Savitski MM, Peschek N, Papenfort K, Olsen RJ, Musser JM, Kumaraswami M

Proceedings of the National Academy of Sciences of the United States of America, 2017

doi:10.1073/pnas.1705972114.

Wilhelm et al. reply.

Wilhelm M, Hahne H, Savitski M, Marx H, Lemeer S, Bantscheff M, Kuster B

Nature, 2017

doi:10.1038/nature22294.

Thermal proteome profiling: unbiased assessment of protein state through heat-induced stability changes.

Mateus A, Määttä TA, Savitski MM

Proteome science, 2017

doi:10.1186/s12953-017-0122-4.

Structure of the mycobacterial ESX-5 type VII secretion system membrane complex by single-particle analysis.

Beckham KS, Ciccarelli L, Bunduc CM, Mertens HD, Ummels R, Lugmayr W, Mayr J, Rettel M, Savitski MM, Svergun DI, Bitter W, Wilmanns M, Marlovits TC, Parret AH, Houben EN

Nature microbiology, 2017

doi:10.1038/nmicrobiol.2017.47.

Thermal profiling reveals phenylalanine hydroxylase as an off-target of panobinostat.

Becher I, Werner T, Doce C, Zaal EA, Tögel I, Khan CA, Rueger A, Muelbaier M, Salzer E, Berkers CR, Fitzpatrick PF, Bantscheff M, Savitski MM

Nature chemical biology, 2016

doi:10.1038/nchembio.2185.

Mutational analysis of GSK3β protein kinase together with kinome-wide binding and stability studies suggest context-dependent recognition of kinases by the chaperone HSP90.

Jin J, Tian R, Pasculescu A, Dai AY, Williton K, Taylor L, Savitski MM, Bantscheff M, Woodgett JR, Colwill K, Pawson T

Molecular and cellular biology, 2016

doi:10.1128/MCB.01045-15.

Thermal proteome profiling monitors ligand interactions with cellular membrane proteins.

Reinhard FB, Eberhard D, Werner T, Franken H, Childs D, Doce C, Savitski MF, Huber W, Bantscheff M, Savitski MM, Drewes G

Nature methods, 2015

doi:10.1038/nmeth.3652.

Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry.

Franken H, Mathieson T, Childs D, Sweetman GM, Werner T, Tögel I, Doce C, Gade S, Bantscheff M, Drewes G, Reinhard FB, Huber W, Savitski MM

Nature protocols, 2015

doi:10.1038/nprot.2015.101.

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets.

Savitski MM, Wilhelm M, Hahne H, Kuster B, Bantscheff M

Molecular & cellular proteomics : MCP, 2015

doi:10.1074/mcp.m114.046995.

Tracking cancer drugs in living cells by thermal profiling of the proteome.

Savitski MM, Reinhard FB, Franken H, Werner T, Savitski MF, Eberhard D, Martinez Molina D, Jafari R, Dovega RB, Klaeger S, Kuster B, Nordlund P, Bantscheff M, Drewes G

Science (New York, N.Y.), 2014

doi:10.1126/science.1255784.

Chemoproteomics reveals time-dependent binding of histone deacetylase inhibitors to endogenous repressor complexes.

Becher I, Dittmann A, Savitski MM, Hopf C, Drewes G, Bantscheff M

ACS chemical biology, 2014

doi:10.1021/cb500235n.

Mass-spectrometry-based draft of the human proteome.

Wilhelm M, Schlegl J, Hahne H, Moghaddas Gholami A, Lieberenz M, Savitski MM, Ziegler E, Butzmann L, Gessulat S, Marx H, Mathieson T, Lemeer S, Schnatbaum K, Reimer U, Wenschuh H, Mollenhauer M, Slotta-Huspenina J, Boese JH, Bantscheff M, Gerstmair A, Faerber F, Kuster B

Nature, 2014

doi:10.1038/nature13319.

Ion coalescence of neutron encoded TMT 10-plex reporter ions.

Werner T, Sweetman G, Savitski MF, Mathieson T, Bantscheff M, Savitski MM

Analytical chemistry, 2014

doi:10.1021/ac500140s.

The commonly used PI3-kinase probe LY294002 is an inhibitor of BET bromodomains.

Dittmann A, Werner T, Chung CW, Savitski MM, Fälth Savitski M, Grandi P, Hopf C, Lindon M, Neubauer G, Prinjha RK, Bantscheff M, Drewes G

ACS chemical biology, 2014

doi:10.1021/cb400789e.

Measuring and managing ratio compression for accurate iTRAQ/TMT quantification.

Savitski MM, Mathieson T, Zinn N, Sweetman G, Doce C, Becher I, Pachl F, Kuster B, Bantscheff M

Journal of proteome research, 2013

doi:10.1021/pr400098r.

Affinity profiling of the cellular kinome for the nucleotide cofactors ATP, ADP, and GTP.

Becher I, Savitski MM, Savitski MF, Hopf C, Bantscheff M, Drewes G

ACS chemical biology, 2013

doi:10.1021/cb3005879.

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present.

Bantscheff M, Lemeer S, Savitski MM, Kuster B

Analytical and bioanalytical chemistry, 2012

doi:10.1007/s00216-012-6203-4.

High-resolution enabled TMT 8-plexing.

Werner T, Becher I, Sweetman G, Doce C, Savitski MM, Bantscheff M

Analytical chemistry, 2012

doi:10.1021/ac301553x.

A selective inhibitor reveals PI3Kγ dependence of T(H)17 cell differentiation.

Bergamini G, Bell K, Shimamura S, Werner T, Cansfield A, Müller K, Perrin J, Rau C, Ellard K, Hopf C, Doce C, Leggate D, Mangano R, Mathieson T, O'Mahony A, Plavec I, Rharbaoui F, Reinhard F, Savitski MM, Ramsden N, Hirsch E, Drewes G, Rausch O, Bantscheff M, Neubauer G

Nature chemical biology, 2012

doi:10.1038/nchembio.957.

Radical a-ions in electron capture dissociation: on the origin of species.

Zubarev RA, Good DM, Savitski MM

Journal of the American Society for Mass Spectrometry, 2012

doi:10.1007/s13361-012-0374-2.

Delayed fragmentation and optimized isolation width settings for improvement of protein identification and accuracy of isobaric mass tag quantification on Orbitrap-type mass spectrometers.

Savitski MM, Sweetman G, Askenazi M, Marto JA, Lang M, Zinn N, Bantscheff M

Analytical chemistry, 2011

doi:10.1021/ac201760x.

Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia.

Dawson MA, Prinjha RK, Dittmann A, Giotopoulos G, Bantscheff M, Chan WI, Robson SC, Chung CW, Hopf C, Savitski MM, Huthmacher C, Gudgin E, Lugo D, Beinke S, Chapman TD, Roberts EJ, Soden PE, Auger KR, Mirguet O, Doehner K, Delwel R, Burnett AK, Jeffrey P, Drewes G, Lee K, Huntly BJ, Kouzarides T

Nature, 2011

doi:10.1038/nature10509.

Increased throughput of proteomics analysis by multiplexing high-resolution tandem mass spectra.

Ledvina AR, Savitski MM, Zubarev AR, Good DM, Coon JJ, Zubarev RA

Analytical chemistry, 2011

doi:10.1021/ac201843e.

Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes.

Bantscheff M, Hopf C, Savitski MM, Dittmann A, Grandi P, Michon AM, Schlegl J, Abraham Y, Becher I, Bergamini G, Boesche M, Delling M, Dümpelfeld B, Eberhard D, Huthmacher C, Mathieson T, Poeckel D, Reader V, Strunk K, Sweetman G, Kruse U, Neubauer G, Ramsden NG, Drewes G

Nature biotechnology, 2011

doi:10.1038/nbt.1759.

Impact of temperature dependent sampling procedures in proteomics and peptidomics--a characterization of the liver and pancreas post mortem degradome.

Scholz B, Sköld K, Kultima K, Fernandez C, Waldemarson S, Savitski MM, Söderquist M, Borén M, Stella R, Andrén P, Zubarev R, James P

Molecular & cellular proteomics : MCP, 2011

doi:10.1074/mcp.m900229-mcp200.

ATP enhances neuronal differentiation of PC12 cells by activating PKCα interactions with cytoskeletal proteins.

Marín-Vicente C, Guerrero-Valero M, Nielsen ML, Savitski MM, Gómez-Fernández JC, Zubarev RA, Corbalán-García S

Journal of proteome research, 2011

doi:10.1021/pr100742r.

Confident phosphorylation site localization using the Mascot Delta Score.

Savitski MM, Lemeer S, Boesche M, Lang M, Mathieson T, Bantscheff M, Kuster B

Molecular & cellular proteomics : MCP, 2011

doi:10.1074/mcp.m110.003830.

Evaluation of data analysis strategies for improved mass spectrometry-based phosphoproteomics.

Savitski MM, Scholten A, Sweetman G, Mathieson T, Bantscheff M

Analytical chemistry, 2010

doi:10.1021/ac102083q.

H-score, a mass accuracy driven rescoring approach for improved peptide identification in modification rich samples.

Savitski MM, Mathieson T, Becher I, Bantscheff M

Journal of proteome research, 2010

doi:10.1021/pr1006813.

Targeted data acquisition for improved reproducibility and robustness of proteomic mass spectrometry assays.

Savitski MM, Fischer F, Mathieson T, Sweetman G, Lang M, Bantscheff M

Journal of the American Society for Mass Spectrometry, 2010

doi:10.1016/j.jasms.2010.01.012.

MS analysis of rheumatoid arthritic synovial tissue identifies specific citrullination sites on fibrinogen.

Hermansson M, Artemenko K, Ossipova E, Eriksson H, Lengqvist J, Makrygiannakis D, Catrina AI, Nicholas AP, Klareskog L, Savitski M, Zubarev RA, Jakobsson PJ

Proteomics. Clinical applications, 2010

doi:10.1002/prca.200900088.

In vitro neurotoxicity of PBDE-99: immediate and concentration-dependent effects on protein expression in cerebral cortex cells.

Alm H, Scholz B, Kultima K, Nilsson A, Andrén PE, Savitski MM, Bergman A, Stigson M, Fex-Svenningsen A, Dencker L

Journal of proteome research, 2010

doi:10.1021/pr900723c.

Unbiased detection of posttranslational modifications using mass spectrometry.

Savitski MF, Savitski MM

Methods in molecular biology (Clifton, N.J.), 2010

doi:10.1007/978-1-60761-842-3_12.

Neuropeptidomic analysis of the embryonic Japanese quail diencephalon.

Scholz B, Alm H, Mattsson A, Nilsson A, Kultima K, Savitski MM, Fälth M, Sköld K, Brunström B, Andren PE, Dencker L

BMC developmental biology, 2010

doi:10.1186/1471-213x-10-30.

Two dimensional mass mapping as a general method of data representation in comprehensive analysis of complex molecular mixtures.

Artemenko KA, Zubarev AR, Samgina TY, Lebedev AT, Savitski MM, Zubarev RA

Analytical chemistry, 2009

doi:10.1021/ac802532j.

Bifurcating fragmentation behavior of gas-phase tryptic peptide dications in collisional activation.

Savitski MM, Fälth M, Fung YM, Adams CM, Zubarev RA

Journal of the American Society for Mass Spectrometry, 2008

doi:10.1016/j.jasms.2008.08.003.

Analytical utility of small neutral losses from reduced species in electron capture dissociation studied using SwedECD database.

Fälth M, Savitski MM, Nielsen ML, Kjeldsen F, Andren PE, Zubarev RA

Analytical chemistry, 2008

doi:10.1021/ac800944u.

Immunoaffinity enrichments followed by mass spectrometric detection for studying global protein tyrosine phosphorylation.

Bergström Lind S, Molin M, Savitski MM, Emilsson L, Aström J, Hedberg L, Adams C, Nielsen ML, Engström A, Elfineh L, Andersson E, Zubarev RA, Pettersson U

Journal of proteome research, 2008

doi:10.1021/pr8000546.

Electron capture/transfer versus collisionally activated/induced dissociations: solo or duet?

Zubarev RA, Zubarev AR, Savitski MM

Journal of the American Society for Mass Spectrometry, 2008

doi:10.1016/j.jasms.2008.03.007.

Identification of dominant signaling pathways from proteomics expression data.

Zubarev RA, Nielsen ML, Fung EM, Savitski MM, Kel-Margoulis O, Wingender E, Kel A

Journal of proteomics, 2008

doi:10.1016/j.jprot.2008.01.004.

SwedCAD, a database of annotated high-mass accuracy MS/MS spectra of tryptic peptides.

Fälth M, Savitski MM, Nielsen ML, Kjeldsen F, Andren PE, Zubarev RA

Journal of proteome research, 2007

doi:10.1021/pr070345h.

On studying protein phosphorylation patterns using bottom-up LC-MS/MS: the case of human alpha-casein.

Kjeldsen F, Savitski MM, Nielsen ML, Shi L, Zubarev RA

The Analyst, 2007

doi:10.1039/b701902e.

Peptide fragmentation and phospho-site detection.

Savitski MM, Fälth M

Expert review of proteomics, 2007

doi:10.1586/14789450.4.4.445.

Relative specificities of water and ammonia losses from backbone fragments in collision-activated dissociation.

Savitski MM, Kjeldsen F, Nielsen ML, Zubarev RA

Journal of proteome research, 2007

doi:10.1021/pr070121z.

Side-chain losses in electron capture dissociation to improve peptide identification.

Savitski MM, Nielsen ML, Zubarev RA

Analytical chemistry, 2007

doi:10.1021/ac0619332.

Backbone carbonyl group basicities are related to gas-phase fragmentation of peptides and protein folding.

Savitski MM, Kjeldsen F, Nielsen ML, Garbuzynskiy SO, Galzitskaya OV, Surin AK, Zubarev RA

Angewandte Chemie (International ed. in English), 2007

doi:10.1002/anie.200603881.

De novo peptide sequencing and identification with precision mass spectrometry.

Frank AM, Savitski MM, Nielsen ML, Zubarev RA, Pevzner PA

Journal of proteome research, 2007

doi:10.1021/pr060271u.

Hydrogen rearrangement to and from radical z fragments in electron capture dissociation of peptides.

Savitski MM, Kjeldsen F, Nielsen ML, Zubarev RA

Journal of the American Society for Mass Spectrometry, 2007

doi:10.1016/j.jasms.2006.09.008.

Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics.

Nielsen ML, Savitski MM, Zubarev RA

Molecular & cellular proteomics : MCP, 2006

doi:10.1074/mcp.m600248-mcp200.

Liquid chromatography at critical conditions: comprehensive approach to sequence-dependent retention time prediction.

Gorshkov AV, Tarasova IA, Evreinov VV, Savitski MM, Nielsen ML, Zubarev RA, Gorshkov MV

Analytical chemistry, 2006

doi:10.1021/ac060913x.

Complementary sequence preferences of electron-capture dissociation and vibrational excitation in fragmentation of polypeptide polycations.

Savitski MM, Kjeldsen F, Nielsen ML, Zubarev RA

Angewandte Chemie (International ed. in English), 2006

doi:10.1002/anie.200601240.

Determination of the location of positive charges in gas-phase polypeptide polycations by tandem mass spectrometry

Kjeldsen F, Savitski MM, Adams CM, Zubarev RA

INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 2006

doi:10.1016/j.ijms.2005.10.009.

ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures.

Savitski MM, Nielsen ML, Zubarev RA

Molecular & cellular proteomics : MCP, 2006

doi:10.1074/mcp.t500034-mcp200.

PhosTShunter: a fast and reliable tool to detect phosphorylated peptides in liquid chromatography Fourier transform tandem mass spectrometry data sets.

Köcher T, Savitski MM, Nielsen ML, Zubarev RA

Journal of proteome research, 2006

doi:10.1021/pr0503836.

New data base-independent, sequence tag-based scoring of peptide MS/MS data validates Mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of MS/MS techniques.

Savitski MM, Nielsen ML, Zubarev RA

Molecular & cellular proteomics : MCP, 2005

doi:10.1074/mcp.t500009-mcp200.

Improving protein identification using complementary fragmentation techniques in fourier transform mass spectrometry.

Nielsen ML, Savitski MM, Zubarev RA

Molecular & cellular proteomics : MCP, 2005

doi:10.1074/mcp.t400022-mcp200.

Proteomics-grade de novo sequencing approach.

Savitski MM, Nielsen ML, Kjeldsen F, Zubarev RA

Journal of proteome research, 2005

doi:10.1021/pr050288x.

Physicochemical properties determining the detection probability of tryptic peptides in Fourier transform mass spectrometry. A correlation study.

Nielsen ML, Savitski MM, Kjeldsen F, Zubarev RA

Analytical chemistry, 2004

doi:10.1021/ac049571q.

Shifted-basis technique improves accuracy of peak position determination in Fourier transform mass spectrometry.

Savitski MM, Ivonin IA, Nielsen ML, Zubarev RA, Tsybin YO, Håkansson P

Journal of the American Society for Mass Spectrometry, 2004

doi:10.1016/j.jasms.2003.12.003.